Chapter 6: Pathways that harvest and store chemical energy PDF

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This note covers concepts for the pathways that harvest and store chemical energy. ...

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Energy is stored in the chemical bonds of molecules, and it can be released and transformed by the metabolic pathways of living cells. There are 5 principles governing Metabolic pathways: ! " 1. Chemical transformations occur in a series of intermediate reactions that form a metabolic ! " " pathway.! " 2. Each reaction is catalyzed by a specific enzyme. ! " 3. Most metabolic pathways are similar in all organisms. ! " 4. In eukaryotes, many metabolic pathways occur inside specific organelles. ! " 5. Each metabolic pathway is controlled by enzymes that can be inhibited or actived.! Metabolism: ! " Sum of all catabolic and anabolic reaction in an organism. ! " Catabolism: breaking molecules down and releasing energy in their bonds. (EXERGONIC)! " Anabolism: building new structures and storing energy in their bonds (ENERGONIC) ! ! ! ! ! ! ! ! ! ! ! ! ! " " " STEPS of metabolism: ! " 1. The food we eat provide our cells with building blocks. ! " 2. Cannot be used directly from diet.! " 3. Purpose of DIGESTION is to break structure down into smaller units.! " 4. These pieces are then imported into cells. ! " 5. Cells are factories that put the pieces back together into new structures. ! Cellular Respiration: the systematic breaking of bonds and energy extraction of glucose, simple ! " proteins, and fats. ! " ALL cells extract chemical energy in the food in the catabolic processes of Cellular respiration or fermentation. ! ! ! ! ! ! ! ! ! ATP (energy currency of the cell) is relatively important in the cell: ! " " " An active cell requires the production of millions of molecules of ATP PER SECOND to drive ! " its biological machinery. Below are some of the activities in the cell that require free energy ! " derived from the hydrolysis of ATP: ! " " 1. Active transport across a membrane. ! " " 2. Condensation reactions that use enzymes to form polymers. ! " " 3. Motor proteins that move vesicles along microtubules. ! !

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An ATP molecule consists of: Adenine (nitrogen containing base) bonded to ribose (a sugar), """""""" " which is attached to a sequence of three phosphate groups. ! ! ATP hydrolysis releases energy:! Some exergonic cellular reactions are coupled with the formation of ATP from ADP and Pi ! (inorganic phosphate). This is an endergonic reaction. The ATP can then be hydrolyzed at other! sites in the cell, releasing free energy to drive endergonic reactions. (SEE diagram from above).! In other words, the hydrolysis of an ATP molecule yields FREE energy, ADP and the inorganic! phosphate ion (Pi). !

What EXACTLY is energy? ! Energy is the capacity to do work. Energy can take many forms: ! 1. Mechanical energy ! 2. Electrical energy ! 3. Light / solar energy ! 4. Chemical energy! " Chemical energy is stored in bonds of molecules. Chemical energy is a clear and definite ! " thing --> it is electrons that are removed from one C-H bond in a molecule and use in the ! " formation of ADP + Pi. " proton potential energy" into the chemical """" " " energy in ATP. This gradient will then be used to make ATP by "oxidative phosphorylation". ! " " 6. As NADH is oxidized to NAD+, it follows with a reduction reaction--> which forms water! " " from oxygen. Oxygen is the final electron acceptor in the ETC!" The reason we breathe ! " " and have a circulatory system is to deliver oxygen to tissues, because oxygens act as an! " " electron receptor, and become reduced in that way. ! " " " " " " " **NO ATP is made during ETC!! ! ! How the ATP synthase adds a phosphate to ADP (Formation of ATP) " 1. The H+ ions passively diffuses through the ATP synthase. ! " 2. As H+ ions flow through the synthase, they change the shape of the ATP! " synthase--> which opens up the active site for an ADP and phosphate to bind. ! " 3. The activated ATP synthase synthesizes a molecule of ATP.! " 4. This method of making ATP is called "oxidative phosphorylation" because the energy to ! " phosphorylate ADP comes from the oxidation of reduced molecules. ! " 5. 32 ATP is produced from a fully oxidized glucose molecule during this process. ! " " 1. Each NADH or FADH2 = 2.5 ATP molecules are formed.! " " 2. Four molecules of reduced CoA produced by each turn of citric acid cycle yield about 10! " " ATPs. ! " " 3. Two molecules of acetyl CoA are produced from each glucose= 20 ATPs. ! " " 4. Also... NADH molecules produced by glycolysis and pyruvate. ! " " " ** Most ATPs are produced by oxidative phosphorylation!! ! What happens if no O2 around to be final electron acceptor? 1. Fermentation will occur! 2. Incomplete oxidation! 3. NADH is then reoxidized by fermentation! 4. Need to regenerate NAD+ ! 5. Waste products: lactic acid/ethanol, and CO2. ! 6. ATP produced: 2 ! ! ! ! ! ! ! !

" " " " " " ! Anaerobic Cellular Respiration (without the present of O2) ! Energy harvesting ends with glycolysis ONLY rather than proceeding onto citric acid cycle and ETC (which requires oxygen). Therefore, those organisms need a way to recycle their energy transfer molecules in a way that doesn't depend on oxygen. ! " 1. The NADH produced during glycolysis needs to regenerate back to NAD+ , so that it can be! " REUSED in glycolysis. --> electron dumping. ! ! " " " " " " There are two fermentation pathways: ! " " 1. Lactic acid fermentation: pyruvate acid accepts electrons from NADH. Then pyruvic acid! " " is turned into another substance: lactic acid. In other words, NADH is used to reduce ! " " pyruvate into lactic acid, when NADH is oxidized to NAD+. ! " " 2. Alcohol fermentation: pyruvate is converted to acetaldehyde when CO2 is released. Then! " " NADH reduces acetaldehyde to ethanol when NADH is oxidized to NAD+. ! ! ! Photosynthesis: The capture and use of energy from sunlight to reduce CO2 into the organic ! Biomolecule glucose. In other words, photosynthesis capture energy from sunlight, and convert this solar energy into chemical energy that is initially stored in a carbohydrates. ! " 1. Photosynthesis (anabolism) is strongly connected to cellular respiration (catabolism). ! " " " A. Photosynthesis: 6CO2 + 12 H2O --> C6H12O6 + 6O2 + 6 H2O. ! " " " " (Endergonic reaction--> plants build the foods we eat.)! " " " " " I.E: Plants store the energy if sunlight in Glucose. Animals eat this glucose. ! " " " B. Cellular respiration C6H12+6CO2 --> 6CO2 + 6H2O ! " " " " (Exergonic reaction--> animals consume plants and break down large molecules.) ! " " " " " I.E: Animals break down glucose and exhale CO2; then consumed by plants.! Two Pathways of photosynthesis: "! 1. Light reactions: convert light energy to chemical energy in the form of ATP, and reduced electron carrier (NADPH). Same as NADH, but with additional phosphate group attached to the sugar of its adenosine. ! 2. Carbon fixation reactions: do not use light directly, but instead use the ATP and NADPH made by ! The light reactions, along with CO2 to produce carbohydrates. ! ! Plant Structures that facilitate photosynthesis: 1. Mesophyll Cell: A single mesophyll cell within a leaf contains all the component parts of plant cells in general (the chloroplasts (an organelle) which is the actual site of photosynthesis. ! 2. Stomata: pores that let carbon dioxide and oxygen to enter and leave. (Water vapor pass out of the membrane). ! 3. Veins: deliver H2O and carry away sugar. There's a waxy/hydrophobic covering in the vein in which prevent unnecessary water loss. ! 4. Chloroplasts: site of photosynthesis ! A. Inner membrane: thylakoids (pancake like-looking). This structure is active during photosynthesis. ! B. Liquid material of the chloroplast: stomata. This structure is active during the second part of photosynthesis "Calvin cycle". ! 5. Thylakoids membranes: completely sealed off from the rest of the cell. This is where photosynthesis starts, with the absorption of sunlight. This structure contains a pigment, called chlorophyll a. Have structures like ETC, and ATP synthase (cellular respiration). ! ! ! ! !

! Features of Chlorophyll a 1. Chlorophyll a is a pigment protein in Thylakoids that absorbs photons light. ! 2. Chlorophyll a absorbs blue and red wavelengths. ! I. A photon is a packet of light energy. Photon has no mass but specific amounts of energy. ! II. A pigment is a molecule that absorbs the energy of photons of a particulate wavelength. The! " wavelengths that are reflected by pigments are known as colors. ! " " - The photon may bounce off the molecule, it may be scattered or reflected. ! " " - The photon may pass through the molecule, it may be transmitted. ! "" - The photon may be absorbed by the molecule, adding energy to the molecule. ! ! 3. Chlorophyll a can absorb light energy of different wavelengths. ! 4. There are several types of chlorophylls. Chlorophyll a is the most common. Chlorophyll a and b differ ! Only slightly in their molecular structures. ! 5. Chlorophyll a absorbs best in red and blue wavelengths (shorter the wavelengths, greater the. """"""" " energy). Green light is being scattered/or reflected. ! 6. Accessory pigments aid chlorophyll in absorbing lights. Accessory pigments absorb light in different! Wavelengths and transfer it to the chlorophylls. ! " " - The accessory pigments protect against photooxidation --> analogous to sunscreen. ! " " - examples of accessory pigments are: carotenoids (B- carotene), and phycobilins. ! ! The reaction center (features of chlorophyll) 1. Photosystem are large complexes of proteins and pigments (light absorbing molecules) that are optimized to harvest light. = a.k.a Energy- absorbing antenna systems. ! 2. Multiple light harvesting complexes (energy absorbing antenna systems) arranged a reaction center that span throughout the thylakoid membrane. ! 3. A reaction center is located at the center of the system. ! A. The light harvesting chlorophylls absorb light and pass the energy on to a chlorophyll in the reaction center. ! ! The photosystems : There are two types of photosystems: photosystem I and photosystem II. Both photosystems contain many pigments to help collect light energy. Inside the reaction center of the photosystem, there is a special pair of chlorophyll molecules:! " " " " " photosystem I: p700 ; photosystem II: P680.! ! Light Reaction (Stage 1): The purpose of a light dependent reaction is to use light energy to make two molecules needed for the next stage of photosynthesis: ATP, and NADPH. Occur at thylakoid membranes of chloroplasts. ! 1. When light energy is absorbed by one of the many pigments in photosystem II, the light energy is passed inward from pigment to pigment until it reached the reaction center. From there, the energy is transferred to P680 (in photosystem II), boosting an electron (P680) to a HIGH energy level. The high energy electron is passed to an acceptor molecule (reduced), and once an electron is lost, it's unstable, so they grab another electron from a different molecule. In this case, the electron is replenished by an electron from water (oxidized). This splitting of water releases the oxygen we inhale. ! 2. The high energy electron travels to ETC, losing energy as it goes. Some of the released energy drives pumping H+ ions from the stroma into the thylakoid interior, building a gradient. As H+ ions flow down their gradient and into the stroma, they pass through ATP synthase, driving ATP production. (Chemiosmois). ! 3. The electron then arrives at photosystem I, and joins the P700 special pair of chlorophylls in the reaction center. When light energy is absorbed by pigments, and pass inward to the reaction center, the electron in P700 is boosted to a very high energy level, and transferred to an acceptor molec le The special pair's missing electron is replaced b a NEW electron from PSII (arri ing ia

ETC). ! 4. The high energy electron travels down a short second leg of the ETC. At the end of the chain, the electron is passed to NADP+ (along with a second electron from the same pathway) to make NADPH! ! ! ! ! ! ! ! ! ! Overall: LT absorption @ PSII --> ATP synthesis --> LT absorption @ PSI--> NADPH formation. MORE to add: ! 1. Once light energy reached the special pair at the photosystem, it loses an electron when excited, passing it another molecule in the complex --> primary electron acceptor. With this transfer, the electron will begin its journey through an electron transport chain. ! 2. As the electron moves through ETC, it goes from higher to a lower energy level, releasing energy. The energy is used to pump protons from outside the thylakoid into the interior of thylakoid.! --> makes ATP. ! 3. Since electrons have lost energy prior to arrival at PSI from pumping H+ ions in ETC, they must be ! " re-engergized through absorption of another photon. ! ! Calvin Cycle (Stage 2) A.K.A: "Carbon Fixation" Energy molecules produced during the first stage of photosynthesis (ATP and NADPH) is used to supply this processes. In Calvin cycle, CO2 is fixed into a reduced form and convert it to carbohydrates. The reactions of the Calvin cycle take place in the stroma ( the inner space of the chloroplasts). The Calvin cycle can be subdivided subdivided into three main stages: carbon fixation, reduction, and regeneration of the starting molecule. ! ! 1. Carbon Fixation: The enzyme "rubisco" drives the below catalyzed reactions--> ! " The cycle starts with one CO2 molecule combines with an acceptor molecule, which is the 5C """"" " ribulose-1,5- bisphosphate (RuBP). This step makes a 6C compound that splits into two """"""""""""""" " molecules of a 3C compound (3-phosphoglyceric acid / 3-PGA). The enzyme rubisco catalyzes """" " two or three Fixation reactions PER SECOND! Because of this reason, plants need a huge supply " of rubisco to perform photosynthesis to satisfy the needs of growth and metabolism. Rubisco """""" " makes up about half of all the proteins in a leaf (MOST abundant protein in the world). ! 2. Reduction: In the second stage, energy molecules (ATP and NADPH) are used to convert the 3 ! " phosphoglyceric acid (3-PGA) This molecule is made from the previous stage (photosynthesis) ! " 3 PGA molecules is converted into molecules of a three carbon sugar phosphate! glyceraldehyde-3-phosphate (G3P). This stage is named as reduction because NADPH donates! " electrons to, or reduces 3-PGA to make G3P. ! 3. Regeneration: Most of the G3P ends up as RuMP (ribulose monophosphate). ATP is used to ! " convert RuMP to RuBP. In order for one G3P molecule to exit the cycle and go towards glucose! " synthesis, three CO2 molecules must enter the cycle, providing three new atoms of fixed carbon. ! " As three CO2 molecules enter the cycle, six G3P molecules are made. From the 6 G3P molecules, " one leaves the cycle to make glucose, the other five must be recycled to regenerate three """"""""""""" " molecules of the RuBP acceptor. ! " ** Every turn of the Calvin cycle, one CO2 is fixed to glucose molecule, and! " the CO2 acceptor from stage one of the Calvin cycle gets regenerated. (ALSO requires ATP). ! " ** Six turns of the Calvin cycle are needed to make 1 glucose molecule. ! !

! What happens to the extra G3P made by the Calvin cycle? ! " 1. Some of the extra G3Ps is exported out to the chloroplast to the cytosolic, where it gets! " converted to hexoses (glucose and fructose). These molecules may be broken down for energy in! " mitochondria as part of cellular respiration, used as carbon skeletons for the synthesis of amino! " acids and other molecules, or converted to sucrose, which is transported out of the leaf to other ! " organs in the plant. ! " 2. After convert to glucose it will be condensed into starch, and also used as structural material ! " (cellulose). This storage of carbohydrate can then be drawn on during the night so that the! " photosynthetic tissues can continue to export sucrose to the rest of the plant. This provides a ! " ready supply of glucose to fuel cellular activities. ! " " " Photosynthesis IS NOT AN EFFICIENT SYSTEM. Only 5% of light energy is captured and stored in carbohydrates. While 95% of energy is lost during photosynthesis....